Variant report

Variant	rs7040949
Chromosome Location	chr9:94975957-94975958
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10115222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10116813	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[ASN][1000 genomes]
rs10120980	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10121495	0.83[EUR][1000 genomes]
rs10123342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125474	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10283572	0.91[CEU][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs10453241	0.81[EUR][1000 genomes]
rs1053441	0.92[CEU][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs1053446	0.92[CEU][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap];0.80[EUR][1000 genomes]
rs10739927	0.92[CEU][hapmap];0.80[JPT][hapmap];0.86[EUR][1000 genomes]
rs10739928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761151	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10761153	0.85[EUR][1000 genomes]
rs10761154	0.92[CEU][hapmap];0.92[YRI][hapmap];0.80[EUR][1000 genomes]
rs10761155	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[ASN][1000 genomes]
rs10761160	0.95[ASN][1000 genomes]
rs10820960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10820961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10820964	0.92[CEU][hapmap];0.80[JPT][hapmap];0.87[EUR][1000 genomes]
rs10820965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820967	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820968	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs10820969	0.92[CEU][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap];0.85[EUR][1000 genomes]
rs10820971	0.92[CEU][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs10992273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992280	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992291	0.87[EUR][1000 genomes]
rs10992303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992304	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs10992319	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992322	0.92[CEU][hapmap];0.80[JPT][hapmap];0.91[YRI][hapmap];0.80[EUR][1000 genomes]
rs1121978	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs1121979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1133908	0.86[EUR][1000 genomes]
rs11791001	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs11792019	0.95[ASN][1000 genomes]
rs11792342	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11792916	1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs12336415	0.95[ASN][1000 genomes]
rs12342019	0.95[ASN][1000 genomes]
rs12353096	0.87[EUR][1000 genomes]
rs1380	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1535756	0.95[ASN][1000 genomes]
rs2007837	0.81[EUR][1000 genomes]
rs2025388	0.92[CEU][hapmap];0.80[JPT][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes]
rs2151618	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274966	0.92[CEU][hapmap];0.80[JPT][hapmap];0.91[YRI][hapmap]
rs2295941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516567	0.81[EUR][1000 genomes]
rs2516568	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2761677	0.98[ASN][1000 genomes]
rs2761678	0.82[ASN][1000 genomes]
rs2761679	0.81[EUR][1000 genomes]
rs2761681	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3758229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780345	0.80[ASN][1000 genomes]
rs3824424	1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs6479416	0.86[EUR][1000 genomes]
rs6479417	0.92[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs6479418	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479419	0.92[CEU][hapmap];0.80[JPT][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes]
rs6479420	0.83[EUR][1000 genomes]
rs6479422	0.95[ASN][1000 genomes]
rs7020874	0.88[CEU][hapmap];0.80[JPT][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes]
rs7023004	0.92[CEU][hapmap];0.80[JPT][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes]
rs7024190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7026361	0.92[CEU][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs7027595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029879	0.83[ASN][1000 genomes]
rs7030920	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs7033979	0.95[ASN][1000 genomes]
rs7042335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7043152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7045409	0.82[EUR][1000 genomes]
rs7045451	0.89[EUR][1000 genomes]
rs7045572	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs7047089	0.92[CEU][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes]
rs710162	0.92[CEU][hapmap];0.80[JPT][hapmap];0.87[EUR][1000 genomes]
rs7847929	0.92[CEU][hapmap];0.80[JPT][hapmap];0.80[EUR][1000 genomes]
rs7848055	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7850432	0.92[CEU][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes]
rs7850528	0.95[ASN][1000 genomes]
rs7853859	0.92[CEU][hapmap];0.80[JPT][hapmap];0.91[YRI][hapmap]
rs7856204	0.81[EUR][1000 genomes]
rs7863406	0.92[CEU][hapmap];0.80[JPT][hapmap];0.86[EUR][1000 genomes]
rs7867909	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7872375	0.92[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs7873397	0.95[ASN][1000 genomes]
rs7873932	0.92[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs9299403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9299404	0.92[CEU][hapmap];0.80[JPT][hapmap];0.91[YRI][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7040949	NOL8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94968800-94976800	Strong transcription	A549	lung
2	chr9:94969600-94976200	Strong transcription	NH-A	brain
3	chr9:94969600-94977000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:94969800-94976400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:94969800-94976800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr9:94970000-94976600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:94970400-94976000	Strong transcription	Hela-S3	cervix
8	chr9:94970400-94976400	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr9:94970400-94976600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr9:94970400-94976600	Strong transcription	Liver	Liver
11	chr9:94970400-94976600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr9:94970400-94976800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr9:94970400-94976800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:94970400-94977200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr9:94970400-94977800	Strong transcription	Primary T cells from cord blood	blood
16	chr9:94970600-94976400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr9:94970600-94976400	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr9:94970600-94976400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr9:94970600-94976400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr9:94970600-94976600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:94970600-94976600	Strong transcription	HMEC	breast
22	chr9:94970800-94976000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
23	chr9:94970800-94976000	Strong transcription	HSMMtube	muscle
24	chr9:94970800-94976200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr9:94970800-94976400	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr9:94970800-94976400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:94970800-94976400	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr9:94970800-94976400	Strong transcription	Brain Substantia Nigra	brain
29	chr9:94970800-94976600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:94970800-94976600	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr9:94970800-94976600	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr9:94970800-94976600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:94970800-94976600	Strong transcription	Brain Germinal Matrix	brain
34	chr9:94970800-94976600	Strong transcription	Brain Hippocampus Middle	brain
35	chr9:94970800-94976600	Strong transcription	Fetal Thymus	thymus
36	chr9:94970800-94976600	Strong transcription	Dnd41	blood
37	chr9:94970800-94976800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr9:94970800-94976800	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr9:94970800-94976800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr9:94970800-94976800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr9:94970800-94976800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr9:94970800-94976800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr9:94970800-94976800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr9:94970800-94976800	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr9:94970800-94976800	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr9:94970800-94983400	Weak transcription	Stomach Mucosa	stomach
47	chr9:94971000-94976000	Strong transcription	GM12878-XiMat	blood
48	chr9:94971000-94976000	Strong transcription	HUVEC	blood vessel
49	chr9:94971000-94976200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr9:94971000-94976200	Strong transcription	Rectal Mucosa Donor 31	rectum

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